Automated extracting of amino acid spin systems in proteins using 3D HCCH-COSY/TOCSY spectroscopy and constrained partitioning algorithm (CPA)

An automated approach has been developed to extract amino acid spin systems from proteins or peptides by analyzing 3D HCCH-COSY/TOCSY spectra through a constrained,partitioning algorithm. The key step in this approach is that two cross peaks are merged to form a spin system not only by sharing one frequency but also by observing additional contraining cross peaks, such as from COSY and/or TOCSY data. The extracted amino acid spin systems show the connectivity relationships between these spins as well as their chemical shifts. This feature differs from other automated spin system extraction programs making it easier to be applied to automatic amino acid recognition applications. The 90 amino acid protein N-domain of chicken skeletal troponin-C (1-90) was used to test the implementation of the algorithm with both simulated and real experimental data. Limitations of the algorithm are discussed.